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Marcello-Sega/pytim

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pytim/patches.py

Summary

Maintainability
A
3 hrs
Test Coverage

Function patchTrajectory has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def patchTrajectory(trajectory, interface):
    """ Patch the MDAnalysis trajectory class

        this patch makes the layer assignement being automatically
        called whenever a new frame is loaded.
Severity: Minor
Found in pytim/patches.py - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function patchMDTRAJ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def patchMDTRAJ(trajectory, universe):
    """ Patch the mdtraj Trajectory class

        automates the data exchange between MDAnalysis and mdtraj classes
Severity: Minor
Found in pytim/patches.py - About 55 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Refactor this function to reduce its Cognitive Complexity from 16 to the 15 allowed.
Open

def patchTrajectory(trajectory, interface):
Severity: Critical
Found in pytim/patches.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Remove this commented out code.
Open

    #       return _openmm.CompoundIntegrator_step(self, steps)
Severity: Major
Found in pytim/patches.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Merge this if statement with the enclosing one.
Open

                        if self.interface._frame != self.frame:
Severity: Major
Found in pytim/patches.py by sonar-python

Merging collapsible if statements increases the code's readability.

Noncompliant Code Example

if condition1:
    if condition2:
        # ...

Compliant Solution

if condition1 and condition2:
    # ...

Line too long (81 > 79 characters)
Open

        trajectory.original_read_frame_with_aux = trajectory._read_frame_with_aux
Severity: Minor
Found in pytim/patches.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

        if not (mdtraj.formats.pdb.PDBTrajectoryFile._atomNameReplacements == {}):
Severity: Minor
Found in pytim/patches.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (94 > 79 characters)
Open

        mdtraj.formats.pdb.PDBTrajectoryFile._loadNameReplacementTables = _NoReplacementTables
Severity: Minor
Found in pytim/patches.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

            return numpy.lib.arraypad._as_pairs(crop_width, ar.ndim, as_index=True)
Severity: Minor
Found in pytim/patches.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (164 > 79 characters)
Open

            print('Warning: mdtraj has not been patched correctly. The trajectory must be loaded *after* importing pytim: some atom names might have been replaced')
Severity: Minor
Found in pytim/patches.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Rename function "_NoReplacementTables" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

        def _NoReplacementTables():
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchTrajectory" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchTrajectory(trajectory, interface):
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchMDTRAJ" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchMDTRAJ(trajectory, universe):
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchMDTRAJ_ReplacementTables" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchMDTRAJ_ReplacementTables():
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchNumpy" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchNumpy():
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchOpenMM" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchOpenMM(simulation, interface):
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

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